3HIE

Structure of the membrane-binding domain of the Sec3 subunit of the Exocyst complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-function study of the N-terminal domain of exocyst subunit Sec3.

Baek, K.Knodler, A.Lee, S.H.Zhang, X.Orlando, K.Zhang, J.Foskett, T.J.Guo, W.Dominguez, R.

(2010) J Biol Chem 285: 10424-10433

  • DOI: https://doi.org/10.1074/jbc.M109.096966
  • Primary Citation of Related Structures:  
    3HIE

  • PubMed Abstract: 

    The exocyst is an evolutionarily conserved octameric complex involved in polarized exocytosis from yeast to humans. The Sec3 subunit of the exocyst acts as a spatial landmark for exocytosis through its ability to bind phospholipids and small GTPases. The structure of the N-terminal domain of Sec3 (Sec3N) was determined ab initio and defines a new subclass of pleckstrin homology (PH) domains along with a new family of proteins carrying this domain. Respectively, N- and C-terminal to the PH domain Sec3N presents an additional alpha-helix and two beta-strands that mediate dimerization through domain swapping. The structure identifies residues responsible for phospholipid binding, which when mutated in cells impair the localization of exocyst components at the plasma membrane and lead to defects in exocytosis. Through its ability to bind the small GTPase Cdc42 and phospholipids, the PH domain of Sec3 functions as a coincidence detector at the plasma membrane.


  • Organizational Affiliation

    Department of Physiology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exocyst complex component SEC3
A, B, C, D
171Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEC3PSL1YER008C
UniProt
Find proteins for P33332 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33332 
Go to UniProtKB:  P33332
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33332
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.697α = 89.9
b = 68.486β = 82.17
c = 68.036γ = 71.79
Software Package:
Software NamePurpose
HKL-2000data collection
SnBphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary